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<H3>7. Example problems 
</H3>
<P>The LAMMPS distribution includes an examples sub-directory with
several sample problems.  Each problem is in a sub-directory of its
own.  Most are 2d models so that they run quickly, requiring at most a
couple of minutes to run on a desktop machine.  Each problem has an
input script (in.*) and produces a log file (log.*) and dump file
(dump.*) when it runs.  Some use a data file (data.*) of initial
coordinates as additional input.  A few sample log file outputs on
different machines and different numbers of processors are included in
the directories to compare your answers to.  E.g. a log file like
log.crack.foo.P means it ran on P processors of machine "foo".
</P>
<P>For examples that use input data files, many of them were produced by
<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
documentation and provided with the LAMMPS distribution.
</P>
<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
text dump file will be produced, which can be animated by various
<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>.  It can
also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
Tools</A> section of the LAMMPS documentation.
</P>
<P>If you uncomment the <A HREF = "dump.html">dump image</A> command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
snapshot images will be produced when the simulation runs.  They can
be quickly post-processed into a movie using commands described on the
<A HREF = "dump_image.html">dump image</A> doc page.
</P>
<P>Animations of many of these examples can be viewed on the Movies
section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
</P>
<P>These are the sample problems in the examples sub-directories:
</P>
<DIV ALIGN=center><TABLE  BORDER=1 >
<TR><TD >body</TD><TD >     body particles, 2d system</TD></TR>
<TR><TD >colloid</TD><TD >  big colloid particles in a small particle solvent, 2d system</TD></TR>
<TR><TD >comb</TD><TD >	  models using the COMB potential</TD></TR>
<TR><TD >crack</TD><TD >	  crack propagation in a 2d solid</TD></TR>
<TR><TD >dipole</TD><TD >   point dipolar particles, 2d system</TD></TR>
<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
<TR><TD >eim</TD><TD >      NaCl using the EIM potential</TD></TR>
<TR><TD >ellipse</TD><TD >  ellipsoidal particles in spherical solvent, 2d system</TD></TR>
<TR><TD >flow</TD><TD >	  Couette and Poiseuille flow in a 2d channel</TD></TR>
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
<TR><TD >gpu</TD><TD >      use of the GPU package for GPU acceleration</TD></TR>
<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
<TR><TD >indent</TD><TD >	  spherical indenter into a 2d solid</TD></TR>
<TR><TD >kim</TD><TD >      use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
<TR><TD >line</TD><TD >     line segment particles in 2d rigid bodies</TD></TR>
<TR><TD >meam</TD><TD >	  MEAM test for SiC and shear (same as shear examples)</TD></TR>
<TR><TD >melt</TD><TD >	  rapid melt of 3d LJ system</TD></TR>
<TR><TD >micelle</TD><TD >  self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
<TR><TD >min</TD><TD >	  energy minimization of 2d LJ melt</TD></TR>
<TR><TD >msst</TD><TD >	  MSST shock dynamics</TD></TR>
<TR><TD >neb</TD><TD >	  nudged elastic band (NEB) calculation for barrier finding</TD></TR>
<TR><TD >nemd</TD><TD >	  non-equilibrium MD of 2d sheared system</TD></TR>
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
<TR><TD >peptide</TD><TD >  dynamics of a small solvated peptide chain (5-mer)</TD></TR>
<TR><TD >peri</TD><TD >	  Peridynamic model of cylinder impacted by indenter</TD></TR>
<TR><TD >pour</TD><TD >     pouring of granular particles into a 3d box, then chute flow</TD></TR>
<TR><TD >prd</TD><TD >      parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >reax</TD><TD >     RDX and TATB models using the ReaxFF</TD></TR>
<TR><TD >rigid</TD><TD >    rigid bodies modeled as independent or coupled</TD></TR>
<TR><TD >shear</TD><TD >    sideways shear applied to 2d solid, with and without a void</TD></TR>
<TR><TD >srd</TD><TD >      stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
<TR><TD >tad</TD><TD >      temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >tri</TD><TD >      triangular particles in rigid bodies 
</TD></TR></TABLE></DIV>

<P>Here is how you might run and visualize one of the sample problems:
</P>
<PRE>cd indent
cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
lmp_linux < in.indent              # run the problem 
</PRE>
<P>Running the simulation produces the files <I>dump.indent</I> and
<I>log.lammps</I>.  You can visualize the dump file as follows:
</P>
<PRE>../../tools/xmovie/xmovie -scale dump.indent 
</PRE>
<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> line(s) in the input
script a series of JPG images will be produced by the run.  These can
be viewed individually or turned into a movie or animated by tools
like ImageMagick or QuickTime or various Windows-based tools.  See the
<A HREF = "dump_image.html">dump image</A> doc page for more details.  E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
</P>
<PRE>% convert -loop 1 *.jpg foo.gif 
</PRE>
<HR>

<P>There is also a COUPLE directory with examples of how to use LAMMPS as
a library, either by itself or in tandem with another code or library.
See the COUPLE/README file to get started.
</P>
<P>There is also an ELASTIC directory with an example script for
computing elastic constants, using a zero temperature Si example.  See
the in.elastic file for more info.
</P>
<P>There is also a USER directory which contains subdirectories of
user-provided examples for user packages.  See the README files in
those directories for more info.  See the
<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
packages.
</P>
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